Modern ultrastructural and molecular studies have provided important information that has led to a reassessment of the evolution of algae. In addition, the fossil record for some groups of algae has hindered evolutionary studies, and the realization that some algae are more closely related to protozoa or fungi than they are to other algae came late, producing confusion in evolutionary thought and delays in understanding the evolution of the algae.

The Euglenophyceae are believed to be an ancient lineage of algae that includes some zooflagellate protozoa, which is supported by ultrastructural and molecular data. Some scientists consider the colourless euglenophytes to be an older group and believe that the chloroplasts were incorporated by symbiogenesis more recently. The order of algae with the best fossil record are the Dasycladales, which are calcified unicellar forms of elegant construction dating back at least to the Triassic Period.

Some scientists consider the red algae, which bear little resemblance to any other group of organisms, to be very primitive eukaryotes that evolved from the prokaryotic blue-green algae. Evidence in support of this view includes the nearly identical photosynthetic pigments and the very similar starches among the red algae and the blue-green algae. Many scientists, however, attribute the similarity to an endosymbiotic origin of the red algal chloroplast from a blue-green algal symbiont. Other scientists suggest that the red algae evolved from the Cryptophyceae, with the loss of flagella, or from fungi by obtaining a chloroplast. In support of this view are similarities in mitosis and in cell wall plugs, special structures inserted into holes in the cell walls that interconnect cells. Some evidence suggests that such plugs regulate the intercellular movement of solutes. Ribosomal gene sequence data from studies in molecular biology suggest that the red algae arose along with animal, fungal, and green plant lineages.

The green algal classes are evolutionarily related, but their origins are unclear. Most consider the class Micromonadophyceae to be the most ancient group, and some fossil data support this view. The class Ulvophyceae is also ancient, whereas the classes Charophyceae and Chlorophyceae are more recent.

The class Dinophyceae is of uncertain origin. During the 1960s and ’70s the unusual structure and chemical composition of the nuclear DNA of the Dinophyceae were interpreted as somewhat primitive features. Some scientists even considered the Dinophyceae to be mesokaryotes (intermediate between the prokaryotes and the eukaryotes); however, this view is no longer accepted. Their peculiar structure is considered as a result of evolutionary divergence, perhaps about 300 or 400 million years ago. The Dinophyceae may be distantly related to the chromophyte algae, but ribosomal gene sequence data suggest that their closest living relatives are the ciliated protozoa. It is likely that the Dinophyceae arose from nonphotosynthetic ancestors and that later some species of Dinophyceae adopted chloroplasts by symbiogenesis and thereby became capable of photosynthesis, although many of these organisms still retain the ability to ingest solid food, similar to protozoa.

The origin of the chromophyte algae also remains unknown. Ultrastructural and molecular data suggest that they are in a protistan lineage that diverged from the protozoa and aquatic fungi about 300 to 400 million years ago. At that time, chloroplasts were incorporated, originally as endosymbionts, and since then the many chromophyte groups have been evolving. Fossil, ultrastructural, and ribosomal gene sequence data support this hypothesis.

The Cryptophyceae are an evolutionary enigma. They have no fossil record, and phylogenetic data are conflicting. Although some workers align them near the red algae, because both groups possess phycobiliproteins in their chloroplasts, most scientists suggest that independent symbiotic origins for the red or blue colour of their chloroplasts could explain the similarity. Cryptophytes have flagellar hairs and other flagellar features that resemble those of the chromophyte algae; however, the mitochondrial structure and other ultrastructural features are distinct and argue against such a relationship.

The fossil record for the algae is not nearly as complete as it is for land plants and animals. Red algal fossils are the oldest known algal fossils. Microscopic spherical algae (Eosphaera and Huroniospora) that resemble the living genus Porphyridium are known from the Gunflint Iron Formation of North America (formed about 1.9 billion years ago). Fossils that resemble modern tetraspores are known from the Amelia Dolomites of Australia (formed some 1.5 billion years ago). The best characterized fossils are the coralline red algae represented in fossil beds since the Precambrian time.

Some of the green algal classes are also very old. Organic cysts resembling modern Micromonadophyceae cysts date from about 1.2 billion years ago. Tasmanites formed the Permian “white coal,” or tasmanite, deposits of Tasmania and accumulated to a depth of several feet in deposits that extend for miles. Similar deposits in Alaska yield up to 150 gallons of oil per ton of sediment. Certain Ulvophyceae fossils that date from about one billion years ago are abundant in Paleozoic rocks. Some green algae deposit calcium carbonate on their cell walls, and these algae produced extensive limestone formations. The Charophyceae, as represented by the large stoneworts (order Charales), date from about 400 million years ago. The oospore, the fertilized female egg, has spirals on its surface that were imprinted by the spiraling protective cells that surrounded the oospore. Oospores from before about 225 million years ago had right-handed spirals, whereas those formed since that time have had left-handed spirals. The reason for the switch remains a mystery.

Fossil Dinophyceae date from the Silurian Period (430 million years ago). Some workers consider at least a portion of the acritarchs, a group of cystlike fossils of unknown affinity, to be Dinophyceae, but few scientists agree with that view. The acritarchs occurred as early as 700 million years ago.

The Chromophyta have the shortest fossil history among the major algal groups. Some scientists believe that the group is ancient, whereas others point out that there is a lack of data to support this view and suggest that the group evolved recently, as indicated by fossil and molecular data. The oldest chromophyte fossils, putative brown algae, are approximately 400 million years old. Coccolithophores, coccolith-bearing members of the Prymnesiophyceae, date from the Late Triassic Epoch (230 to 200 228.7 to 199.6 million years ago), with one reported from approximately 280 million years ago. Coccolithophores were extremely abundant during the Mesozoic Era, contributing to deep deposits such as those that constitute the white cliffs of southeast England. Most species became extinct at the end of the Cretaceous Period (65.5 million years ago), along with the dinosaurs, and indeed there are more extinct species of coccolithophores than there are living species. The Chrysophyceae, Bacillariophyceae, and Dictyochophyceae date from about 100 million years ago, and despite the mass extinctions 65.5 million years ago, many species still flourish. In Lompoc, Calif., U.S., their siliceous remains have formed deposits of diatomite almost 0.5 km (0.3 mile) in depth, while at Mývatn in Iceland the lake bottom bears significant amounts of diatomite in the form of diatomaceous ooze, many metres in depth.

The Xanthophyceae may be even more recent, with fossils dating from about 20 million years ago, while fossil records of the remaining groups of algae, notably the Euglenophyceae and the Cryptophyuceae, which lack mineralized walls, are negligible.